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Eck S, Wörz S, Müller-Ott K, Hahn M, Biesdorf A, Schotta G, Rippe K, Rohr K. A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci. Med Image Anal 2016; 32:18-31. [DOI: 10.1016/j.media.2016.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 03/07/2016] [Accepted: 03/09/2016] [Indexed: 12/01/2022]
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Maison C, Bailly D, Quivy JP, Almouzni G. The methyltransferase Suv39h1 links the SUMO pathway to HP1α marking at pericentric heterochromatin. Nat Commun 2016; 7:12224. [PMID: 27426629 PMCID: PMC4960310 DOI: 10.1038/ncomms12224] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/10/2016] [Indexed: 02/03/2023] Open
Abstract
The trimethylation of histone H3 on lysine 9 (H3K9me3) – a mark recognized by HP1 that depends on the Suv39h lysine methyltransferases (KMTs) – has provided a basis for the reader/writer model to explain HP1 accumulation at pericentric heterochromatin in mammals. Here, we identify the Suv39h1 paralog, as a unique enhancer of HP1α sumoylation both in vitro and in vivo. The region responsible for promoting HP1α sumoylation (aa1–167) is distinct from the KMT catalytic domain and mediates binding to Ubc9. Tethering the 1–167 domain of Suv39h1 to pericentric heterochromatin, but not mutants unable to bind Ubc9, accelerates the de novo targeting of HP1α to these domains. Our results establish an unexpected feature of Suv39h1, distinct from the KMT activity, with a major role for heterochromatin formation. We discuss how linking Suv39h1 to the SUMO pathway provides conceptual implications for our general view on nuclear domain organization and physiological functions. The Suv39h histone methyltransferases promote trimethylation of histone H3 on lysine 9 (H3K9me3). Here, in the Suv39h1 paralog, the authors identify an enhancer of HP1a sumoylation activity that impacts heterochromatin.
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Affiliation(s)
- Christèle Maison
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Delphine Bailly
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
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Romeo K, Louault Y, Cantaloube S, Loiodice I, Almouzni G, Quivy JP. The SENP7 SUMO-Protease Presents a Module of Two HP1 Interaction Motifs that Locks HP1 Protein at Pericentric Heterochromatin. Cell Rep 2015; 10:771-782. [PMID: 25660026 DOI: 10.1016/j.celrep.2015.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/08/2014] [Accepted: 12/24/2014] [Indexed: 12/17/2022] Open
Abstract
HP1 enrichment at pericentric heterochromatin is essential for proper chromosome segregation. While H3K9me3 is thought to be a major contributor to HP1 enrichment at pericentric domains, in mouse cells, the SUMO-protease SENP7 is required in addition to H3K9me3. How this is achieved remains elusive. Here, we find that loss of SENP7 leads to an increased time spent in mitosis. Furthermore, we reveal that a short module comprising two consecutive HP1 interaction motifs on SENP7 is the determinant for HP1 enrichment and acts by restricting HP1 mobility at pericentric domains. We propose a mechanism for maintenance of HP1 enrichment in which this module functions on top of H3K9me3 to lock contiguous HP1 molecules already docked on H3K9me3-modified nucleosomes. H3K9me3 would thus promote HP1 enrichment only if a locking system is in place. This mechanism may apply to other nuclear domains to contribute to the control of genome plasticity and integrity.
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Affiliation(s)
- Kelly Romeo
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Yann Louault
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Isabelle Loiodice
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
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Müller-Ott K, Erdel F, Matveeva A, Mallm JP, Rademacher A, Hahn M, Bauer C, Zhang Q, Kaltofen S, Schotta G, Höfer T, Rippe K. Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol 2014; 10:746. [PMID: 25134515 PMCID: PMC4299515 DOI: 10.15252/msb.20145377] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The cell establishes heritable patterns of active and silenced chromatin via interacting factors
that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we
have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts.
We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in
living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2
demarcate the PCH state. From the experimental data, we developed a predictive mathematical model
that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a
spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin
dynamics. This “nucleation and looping” mechanism is particularly robust toward
transient perturbations and stably maintains the PCH state. These features make it an attractive
model for establishing functional epigenetic domains throughout the genome based on the localized
immobilization of chromatin-modifying enzymes.
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Affiliation(s)
- Katharina Müller-Ott
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Fabian Erdel
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anna Matveeva
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Anne Rademacher
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Matthias Hahn
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Caroline Bauer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Qin Zhang
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Sabine Kaltofen
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
| | - Gunnar Schotta
- Munich Center for Integrated Protein Science and Adolf Butenandt Institute, Ludwig Maximilians University, Munich, Germany
| | - Thomas Höfer
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Division Theoretical Systems Biology, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Heidelberg, Germany
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Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G. The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle. J Cell Sci 2014; 127:3347-59. [PMID: 24906798 DOI: 10.1242/jcs.148189] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.
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Affiliation(s)
- Ekaterina Boyarchuk
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Isabelle Vassias
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
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Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript. Cell Rep 2013; 4:1156-67. [PMID: 24055057 DOI: 10.1016/j.celrep.2013.08.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/02/2013] [Accepted: 08/08/2013] [Indexed: 02/05/2023] Open
Abstract
The equalization of pericentric heterochromatin from distinct parental origins following fertilization is essential for genome function and development. The recent implication of noncoding transcripts in this process raises questions regarding the connection between RNA and the nuclear organization of distinct chromatin environments. Our study addresses the interrelationship between replication and transcription of the two parental pericentric heterochromatin (PHC) domains and their reorganization during early embryonic development. We demonstrate that the replication of PHC is dispensable for its clustering at the late two-cell stage. In contrast, using parthenogenetic embryos, we show that pericentric transcripts are essential for this reorganization independent of the chromatin marks associated with the PHC domains. Finally, our discovery that only reverse pericentric transcripts are required for both the nuclear reorganization of PHC and development beyond the two-cell stage challenges current views on heterochromatin organization.
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Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes. J Mol Biol 2012; 425:54-70. [PMID: 23142645 DOI: 10.1016/j.jmb.2012.10.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 11/22/2022]
Abstract
The majority of the genome in eukaryotes is packaged into transcriptionally inactive chromatin. Heterochromatin protein 1 (HP1) is a major player in the establishment and maintenance of heterochromatin. HP1 specifically recognizes a methylated lysine residue at position 9 in histone H3 through its N-terminal chromo domain (CD). To elucidate the binding properties of HP1α to nucleosomes in vitro, we reconstituted nucleosomes containing histone H3 trimethylated at lysine 9. HP1α exhibited high-affinity binding to nucleosomes containing methylated histone H3 in a nucleosome core-number-dependent manner. The hinge region (HR) connecting the CD and C-terminal chromoshadow domain (CSD), and the CSD contributed to the selective binding of HP1α to histone H3 with trimethylated lysine 9 through weak DNA binding and by suppressing the DNA binding, respectively. We propose that not only the specific recognition of lysine 9 methylation of histone H3 by the CD but also the HR and the CSD cooperatively contribute to the selective binding of HP1α to histone H3 lysine 9 methylated nucleosomes.
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